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PVT1 Pvt1 oncogene [ Homo sapiens (human) ]

Gene ID: 5820, updated on 17-Jun-2024

Summary

Official Symbol
PVT1provided by HGNC
Official Full Name
Pvt1 oncogeneprovided by HGNC
Primary source
HGNC:HGNC:9709
See related
Ensembl:ENSG00000249859 MIM:165140; AllianceGenome:HGNC:9709
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TP53LC09; LINC00079; MIR1204HG; NCRNA00079; onco-lncRNA-100
Summary
This gene represents a long non-coding RNA locus that has been identified as a candidate oncogene. Increased copy number and overexpression of this gene are associated with many types of cancers including breast and ovarian cancers, acute myeloid leukemia and Hodgkin lymphoma. Allelic variants of this gene are also associated with end-stage renal disease attributed to type 1 diabetes. Consistent with its association with various types of cancer, transcription of this gene is regulated by the tumor suppressor p53 through a canonical p53-binding site, and it has been implicated in regulating levels of the proto-oncogene MYC to promote tumorigenesis. [provided by RefSeq, Sep 2015]
Expression
Broad expression in ovary (RPKM 3.9), bone marrow (RPKM 3.4) and 21 other tissues See more
Orthologs
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Genomic context

See PVT1 in Genome Data Viewer
Location:
8q24.21
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (127794524..128101256)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (128922013..129229130)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (128806779..129113499)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128717643-128718143 Neighboring gene NANOG hESC enhancer GRCh37_chr8:128744882-128745383 Neighboring gene origin of replication upstream of MYC Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19530 Neighboring gene cancer susceptibility 11 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:128754894-128756093 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128805180-128805750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19533 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128806893-128807462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128807463-128808034 Neighboring gene MYC proto-oncogene, bHLH transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128814781-128815422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128815423-128816064 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:128816065-128816704 Neighboring gene Sharpr-MPRA regulatory region 14038 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128821670-128822570 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128822571-128823470 Neighboring gene Sharpr-MPRA regulatory region 15510 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128830247-128830786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128832947-128833486 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:128834567-128835106 Neighboring gene microRNA 1204 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:128858753-128858938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128862019-128862636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128864303-128865152 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:128866418-128867617 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128879341-128879948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128888845-128889392 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:128891961-128892128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128893083-128893582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27951 Neighboring gene Sharpr-MPRA regulatory region 1737 Neighboring gene CRISPRi-validated MYC e1 enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128913423-128914077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128916503-128917004 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128920055-128920986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128920987-128921919 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:128923753-128924342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128932048-128932575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128936915-128937414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128951647-128952169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:128969595-128970406 Neighboring gene CRISPRi-validated MYC e2 enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:128976545-128977156 Neighboring gene long intergenic non-protein coding RNA 2912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:129004541-129005042 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:129005043-129005542 Neighboring gene microRNA 1205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:129013561-129014142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27958 Neighboring gene RNA, variant U1 small nuclear 32 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:129037427-129037927 Neighboring gene RNA, U4 small nuclear 25, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:129050073-129050724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:129050725-129051374 Neighboring gene microRNA 1206 Neighboring gene CRISPRi-validated MYC e3 enhancer Neighboring gene CRISPRi-validated MYC e4 enhancer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:129074055-129074702 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:129077402-129078601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19536 Neighboring gene microRNA 1207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:129118718-129119218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:129121159-129122087 Neighboring gene uncharacterized LOC124902020 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:129179416-129180615 Neighboring gene Sharpr-MPRA regulatory region 6197 Neighboring gene microRNA 1208

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
A common variant at 8q24.21 is associated with renal cell cancer.
EBI GWAS Catalog
A genome-wide association study of Hodgkin's lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3).
EBI GWAS Catalog
Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.
EBI GWAS Catalog
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
EBI GWAS Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
EBI GWAS Catalog
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
EBI GWAS Catalog
Genome-wide Association Study Identifies Five Susceptibility Loci for Follicular Lymphoma outside the HLA Region.
EBI GWAS Catalog
Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma.
EBI GWAS Catalog
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
EBI GWAS Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
EBI GWAS Catalog
Genome-wide association study of atypical psychosis.
EBI GWAS Catalog
Genome-wide association study yields variants at 20p12.2 that associate with urinary bladder cancer.
EBI GWAS Catalog
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
EBI GWAS Catalog
Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study.
EBI GWAS Catalog
Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Other Names

  • CXCR4/PVT1 fusion
  • HIST1H2BD/PVT1 fusion
  • MIR1204, MIR1205, MIR1206 and MIR1207 host
  • Oncogene PVT-1 (MYC activator)
  • PVT1/CASC8 fusion
  • PVT1/CCDC26 fusion
  • PVT1/IFRD1 fusion
  • PVT1/IRF2BP2 fusion
  • PVT1/LINC00824 fusion
  • PVT1/MYC fusion
  • PVT1/NFIL3 fusion
  • PVT1/NSMCE2 fusion
  • PVT1/SPRY2 fusion
  • PVT1/UBB fusion
  • Pvt1 oncogene (non-protein coding)
  • RP11-89K10/PVT1 fusion
  • long intergenic non-protein coding RNA 79
  • plasmacytoma variant translocation 1
  • pvt-1 (murine) oncogene homolog, MYC activator

Clone Names

  • MGC21751

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_003367.4 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
    Related
    ENST00000513868.6
  2. NR_186119.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  3. NR_186120.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  4. NR_186121.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  5. NR_186123.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  6. NR_186124.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  7. NR_186125.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  8. NR_186126.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  9. NR_186127.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  10. NR_186128.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  11. NR_186129.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  12. NR_186130.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  13. NR_186131.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  14. NR_186132.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  15. NR_186133.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  16. NR_186134.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  17. NR_186135.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  18. NR_186136.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  19. NR_186137.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  20. NR_186138.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  21. NR_186139.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC103705, AC103819
  22. NR_186140.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  23. NR_186141.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
    Related
    ENST00000660631.1
  24. NR_186142.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  25. NR_186143.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  26. NR_186144.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  27. NR_186145.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  28. NR_186146.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  29. NR_186147.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  30. NR_186148.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  31. NR_186149.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  32. NR_186150.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  33. NR_186151.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  34. NR_186152.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  35. NR_186153.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  36. NR_186154.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  37. NR_186155.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  38. NR_186156.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  39. NR_186157.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  40. NR_186158.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  41. NR_186159.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  42. NR_186160.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  43. NR_186161.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  44. NR_186162.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
    Related
    ENST00000667305.1
  45. NR_186163.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  46. NR_186164.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  47. NR_186165.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  48. NR_186166.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
  49. NR_186167.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
    Related
    ENST00000652816.1
  50. NR_186168.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819
    Related
    ENST00000662413.1
  51. NR_190187.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC026248, AC084123, AC103705, AC103819

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    127794524..128101256
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    128922013..129229130
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)